add "prefix=" option to commands

Feature requests
1

In mothur, it is generally not possible to define the name of the output files. They are just inherited from the input files, with endless (but necessary, I agree) suffixes. Therefore, when performing several analyses starting from the same input files but with different parameters, the older files are overwritten. In general, the possibility to differentiate the output files would also simplify their organization and the usage of batch files.
A simple solution would be to add a “prefix=” option to most (all?) of the commands, that would add a prefix to the output files names.
What do you think about it?
Best regards,
Bernard

2

You could use the set.dir command to redirect the outputs of the different batch files.

set.dir(input=…/yourInputFilesLocation, output=…/batchFile1Folder)
other mothur commands…

3

Thanks for your answer! Actually, I found the set.dir command 10 min ago. Well, before asking new questions, I will go through all the mothur commands first…
Best regards,
Bernard